necom Documentation

Replace node names or append annotations in a Newick file using a TSV file.

Input:

• A Newick tree file.
• A TSV file with 2 or more columns: <original_name> <replacement> [additional_annotations...].

Notes:

• The behavior of the 2nd column (<replacement>) depends on --mode:
  • label (default): replaces the node name. An empty string removes the name.
  • taxid: appends as NCBI TaxID (:T=<replacement>) in NHX.
  • species: appends as species name (:S=<replacement>) in NHX.
  • asis: appends as comments/properties. Values containing = are parsed as key=value pairs; bare values are stored as keys with empty values.
• Columns 3+ are always appended to the node’s comments/properties. Key-value pairs (e.g., color=red) are stored as properties; simple tags (e.g., highlight) are stored as keys with empty values.
• -I, --internal: skip internal nodes (don’t replace/annotate them).
• -L, --leaf: skip leaf nodes (don’t replace/annotate them).

Examples:

1. Basic renaming of nodes necom nwk replace input.nwk --replace-tsv names.tsv > output.nwk

2. Add species and color annotations necom nwk replace input.nwk --replace-tsv annotations.tsv --mode species

3. Remove node names (2nd column is empty) necom nwk replace input.nwk --replace-tsv remove.tsv